One can now produce a Makefile.conf and a sourceme.sh
using autoconf. Just type:

./configure

Or maybe

./configure CXX=icpc

In case you want to use mpi, just use:

./configure CXX=mpic++

Everything should be smooth. I took care that the generated Makefile.conf
is compatible with those stored in configurations/. In this way,
one can always resort to a saved configuration file. Moreover,
jumping between git branches (without need of reconfiguring) will be
easier.

More info on the manual page (no need to use autoconf to compile
the manual and see that page)

Closes #46

I fixed the usage of stopflag in driver so that it is clearer
that the program stops at the end of the present step and not
at the beginning of the following. This is obviously equivalent,
but shows that scope of the flag can be reduced to be defined
at the inner of the MD loop.

Even if this is not a bux fix, I consider it as paired with fix #47
and I merge it to v2.0

The code was crashing with an error during exchange steps when
not using a neighbor list.  It now only crashes if the neighbor list
frequency is not the same as the exchange step frequency.  This is
as it should be.

(should be checked by GT)

This test shows a problem in reweighting (discussed in #48).
In particular, histoA and histoB in this regtest should not
come out identical as they do.

I think this is more coherent with other cmd() calls.

MultiColvarFunction allows you to calculate thing like the average coordination
number for the atoms an sphere centred on a particular atom.  If crystallization
is installed you can also use it to calculate things like the local q4 parameter.

Neighbor list in multicolvar now has three input parameters

TOL - all values less than this are ignored
NL_TOL - all values less than this are ignored until next neighbor list time
NL_STRIDE - frequency with which to update neighbor list

Neighbor list has been tested for DISTANCES and ANGLES.  Still needs more
testing

Closes #14

The interface to set replica communicator from fortran was missing.

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

gro and xyz files can be written with a requested precision.
Notice that gro files produced in this way do not satisfy the official
documentation of gro format, but still work with e.g. vmd, gromacs,
and plumed driver

Closes #36

It just prints a meaningful error.